Contacts of the helix formed by residues 13 - 26 (chain R) in PDB entry 4M8B
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 13 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11R ILE* 4.0 5.2 - - - +
12R ASP* 1.3 83.1 - - - +
14R GLU* 1.3 65.2 + - - +
15R GLN* 3.6 18.4 + - - +
16R ASP* 3.2 23.2 + - - +
17R LEU* 3.2 9.2 + - - +
78R PHE* 4.6 9.2 - - - -
156R ARG* 2.8 27.4 + - - -
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Residues in contact with GLU 14 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13R ASP* 1.3 74.8 + - + +
15R GLN* 1.3 59.0 + - - +
17R LEU* 3.6 18.8 - - + +
18R ALA* 2.9 30.5 + - - +
77R LYS* 2.8 40.7 + - + +
78R PHE* 6.2 1.3 - - + -
121R PHE* 5.8 1.1 - - + -
173R LEU* 4.9 6.5 - - + +
176R LEU* 3.4 37.6 - - + +
177R GLN* 3.7 7.6 + - - +
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Residues in contact with GLN 15 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13R ASP* 3.2 18.4 + - - +
14R GLU* 1.3 75.4 - - - +
16R ASP* 1.3 66.1 + - - +
18R ALA* 3.5 0.9 + - - +
19R LEU* 3.3 36.7 + - - +
156R ARG* 5.3 0.4 - - - +
158R SER* 4.0 18.8 - - - -
168R PRO* 3.9 25.3 - - - +
173R LEU* 4.3 19.1 - - - +
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Residues in contact with ASP 16 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11R ILE* 4.0 7.2 - - + -
12R ASP 3.1 23.7 + - - +
13R ASP* 3.2 14.4 + - - +
15R GLN* 1.3 76.3 - - - +
17R LEU* 1.3 64.8 + - - +
18R ALA 3.4 0.2 + - - -
19R LEU* 3.5 3.1 + - - +
20R VAL* 3.3 26.8 + - - +
156R ARG* 2.8 28.9 + - - +
157R PRO* 3.4 23.0 - - + +
158R SER* 2.6 37.0 + - - +
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Residues in contact with LEU 17 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11R ILE* 3.8 8.5 - - + +
13R ASP 3.2 4.3 + - - +
14R GLU* 3.6 20.4 - - + +
15R GLN 3.3 0.2 - - - -
16R ASP* 1.3 77.8 - - - +
18R ALA* 1.3 63.0 + - - +
20R VAL* 3.2 7.0 + - - +
21R PHE* 3.0 39.5 + - + -
78R PHE* 3.5 32.8 - - + -
121R PHE* 3.4 50.5 - - + -
140R LEU* 3.4 29.8 - - + -
176R LEU* 4.6 4.9 - - + -
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Residues in contact with ALA 18 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14R GLU 2.9 18.3 + - - +
15R GLN* 3.8 4.5 - - - +
17R LEU* 1.3 75.3 - - - +
19R LEU* 1.3 57.5 + - - +
21R PHE* 4.6 0.7 - - - -
22R GLN* 2.9 32.4 + - - +
168R PRO* 3.4 31.0 - - + -
172R LEU* 3.4 9.4 - - + +
173R LEU* 4.3 7.9 - - + -
176R LEU* 3.7 19.5 - - + -
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Residues in contact with LEU 19 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15R GLN* 3.3 27.1 + - - +
16R ASP 3.8 4.3 - - - +
17R LEU 3.3 0.4 - - - -
18R ALA* 1.3 78.2 - - - +
20R VAL* 1.3 56.5 + - - +
22R GLN 3.5 0.2 + - - -
23R GLY* 2.9 24.9 + - - -
157R PRO* 3.7 9.2 - - + +
158R SER* 3.4 39.7 - - - +
163R PHE* 3.4 33.4 - - + +
164R HIS* 5.0 4.5 - - + +
166R PHE* 3.2 36.1 - - - +
167R ARG* 3.9 8.3 - - - +
168R PRO* 4.1 6.5 - - + -
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Residues in contact with VAL 20 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6R THR* 5.1 0.7 - - + -
7R CYS* 3.8 30.3 - - - -
11R ILE* 4.0 12.6 - - + -
16R ASP 3.3 14.8 - - - +
17R LEU* 3.2 6.6 + - - +
19R LEU* 1.3 75.7 - - - +
21R PHE* 1.3 62.1 + - - +
23R GLY 3.2 1.9 + - - -
24R VAL* 3.0 26.9 + - + +
29R LEU* 3.5 12.2 - - + +
50R ILE* 4.5 1.8 - - + -
52R VAL* 3.8 26.0 - - + -
140R LEU* 4.1 10.8 - - + -
157R PRO* 3.9 19.5 - - + -
163R PHE* 4.3 3.6 - - + -
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Residues in contact with PHE 21 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17R LEU* 3.0 31.4 + - + +
18R ALA* 3.9 3.8 - - - +
20R VAL* 1.3 76.1 - - - +
22R GLN* 1.3 56.9 + - - +
24R VAL* 3.0 6.2 + - + +
25R PHE* 2.8 44.6 + + + -
52R VAL* 4.2 21.3 - - + -
121R PHE* 3.8 33.2 - + - -
123R LEU* 3.7 30.1 - - + -
138R PHE* 3.8 29.2 - + + -
140R LEU* 4.0 23.1 - - + -
172R LEU* 4.0 12.1 - - + -
176R LEU* 4.3 6.7 - - + -
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Residues in contact with GLN 22 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18R ALA 2.9 20.5 + - - +
19R LEU 3.8 0.2 - - - +
21R PHE* 1.3 75.3 - - - +
23R GLY* 1.3 57.8 + - - +
25R PHE* 3.2 17.0 + - - +
26R ASN* 2.9 65.5 + - - +
166R PHE* 3.2 28.0 - - - +
167R ARG 3.5 14.8 - - - +
168R PRO* 4.3 1.1 - - + -
169R SER* 3.2 31.8 + - - -
172R LEU* 3.8 10.3 - - + +
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Residues in contact with GLY 23 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19R LEU 2.9 12.2 + - - -
20R VAL 3.2 4.9 + - - -
22R GLN* 1.3 76.9 - - - +
24R VAL* 1.3 58.0 + - - +
26R ASN* 3.8 0.7 + - - +
27R GLY 3.3 2.3 + - - -
28R ASN* 3.1 13.7 + - - +
29R LEU* 3.0 30.0 + - - -
166R PHE* 3.4 30.7 - - - +
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Residues in contact with VAL 24 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6R THR* 4.1 15.7 - - + -
20R VAL* 3.0 18.8 + - + +
21R PHE* 3.0 10.6 + - - +
23R GLY* 1.3 76.3 - - - +
25R PHE* 1.3 73.2 + - + +
27R GLY* 3.2 13.3 + - - -
29R LEU* 3.5 29.9 - - + +
31R CYS* 4.5 16.8 - - + +
52R VAL* 4.2 26.9 - - + -
138R PHE* 5.0 8.5 - - + -
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Residues in contact with PHE 25 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21R PHE* 2.8 33.3 + + + -
22R GLN* 3.6 25.8 - - - +
24R VAL* 1.3 80.6 - - + +
26R ASN* 1.3 62.4 + - - +
27R GLY* 4.6 0.3 - - - -
123R LEU* 4.4 2.7 - - + -
125R PHE* 3.7 28.3 - + - -
127R MET* 3.6 26.4 - - + +
138R PHE* 3.5 44.0 - + - -
169R SER* 6.0 0.4 - - - -
172R LEU* 3.8 22.2 - - + -
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Residues in contact with ASN 26 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22R GLN* 2.9 47.5 + - - +
23R GLY* 4.1 2.9 - - - +
25R PHE* 1.3 78.0 - - - +
27R GLY* 1.3 58.6 + - - +
28R ASN* 3.3 18.7 + - - +
165R LYS 4.2 9.5 + - - -
166R PHE* 4.1 15.6 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il